Jerzy Wieslaw Kozyra

Nanovery

The scaffolded origami technique is an attractive tool for engineering nucleic acid nanostructures. This paper demonstrates scaffolded RNA origami folding in vitro in which, for the first time, all components are transcribed simultaneously in a single-pot reaction. Double-stranded DNA sequences are transcribed by T7 RNA polymerase into scaffold and...

As DNA sequencing and synthesis become cheaper and more easily accessible, the scale and complexity of biological engineering projects is set to grow. Yet, although there is an accelerating convergence between biotechnology and digital technology, a deficit in software and laboratory techniques diminishes the ability to make biotechnology more agil...

The scaffolded origami technique has provided an attractive tool for engineering nucleic acid nanostructures. This paper demonstrates scaffolded RNA origami folding in vitro in which all components are transcribed simultaneously in a single-pot reaction. Double-stranded DNA sequences are transcribed by T7 RNA polymerase into scaffold and staple str...

As DNA sequencing and synthesis become cheaper and more easily accessible, the scale and complexity of biological engineering projects is set to grow. Yet, although there is an accelerating convergence between biotechnology and computing science, a deficit in software and laboratory techniques diminishes the ability to make biotechnology more agile...

Design of experiments (DOE) enables scientists to explore complex, multidimensional spaces against a background of experimental variability with the minimum of resource. While these methods are most successful when combined with expert knowledge to define the design space and capture the dimensionality of the problem, many scientists believe, often...

Data to support Data Availability Statement Harold Fellermann, Ben Shirt-Ediss, Jerzy W Koryza, Matthew Linsley, Dennis W Lendrem, John D Isaacs, Thomas J Howard 2019 Design of Experiments and the Virtual PCR Simulator: an online game for pharmaceutical scientists and biotechnologists. Pharmaceutical Statistics, In press.

Our PCR Simulator is a web-based application designed to introduce concepts of multi-factorial experimental design and support teaching of the polymerase chain reaction. Learners select experimental settings and receive results of their simulated reactions quickly, allowing rapid iteration between data generation and analysis. This enables the stud...

RNA presents intringuing roles in many cellular processes and its versatility underpins many different applications in synthetic biology. Nonetheless, RNA origami as a method for nanofabrication is not yet fully explored and the majority of RNA nanostructures are based on natural pre-folded RNA. Here we describe a biologically inert and uniquely ad...

We recently reported the design for a DNA nano-device that can record and store molecular signals. Here we present an evolutionary algorithm tailored to optimising nucleic acid sequences that predictively fold into our desired target structures. In our approach, a DNA device is first specified abstractly: the topology of the individual strands and...

Nanotechnology and synthetic biology are rapidly converging, with DNA origami being one of the leading bridging technologies. DNA origami was shown to work well in a wide array of biotic environments. However, the large majority of extant DNA origami scaffolds utilize bacteriophages or plasmid sequences thus severely limiting its future applicabili...

We present an implementation of an in vitro signal recorder based on DNA assembly and strand displacement. The signal recorder implements a stack data structure in which both data as well as operators are represented by single stranded DNA " bricks ". The stack grows by adding push and write bricks and shrinks in last-in-first-out manner by adding...